All in one packages (the good, the bad, the ugly)

I remember providing instructions on installing "all in one" packages for Windows systems - like anaconda, canopy and so on -

1) The good - well, they are all in one - so no need to look around for packages to install - you have everything you need in one grand package
2) The bad - sometimes, a package in that all in one may be buggy - and you may want to use an older version (or a newer version) - well, I am sure you can install any version of any package - but it may not be that easy (!) ... I discovered for example that the latest/greatest openpyxl package (functions to read/write xlsx files) has some bugs - and I discovered (accidentally) that 1.6.2 worked as I wanted to (and not the 2.x.x versions)
3) The ugly - often you may not know in any all in one package as to where the problem is - so if you install package by package you can debug easily

How to do X? (add your own please!)

Here is a list of "X" (please add your own) (I would be happy to share my solutions/explain them)

1) Read a data file (containing rows and columns)
2) Plot one column of data against another column of data
3) plot data from one row against another row
4) Do a linear least squares fit (e.g. Y versus X) - calculate slope, intercept
5) Do a polynomial fit (Y versus X) (plot the data)
6) Read a protein (or DNA/RNA) sequence (from a data file in fasta OR genbank or ... formats)
7) Get information about a protein (or DNA/RNA) sequence (length of sequence, C+G, etc)
8) Read/write excel file (as xlsx, csv, txt)na
9) Solve vapor/liquid equilibrium problems (Antoine's equation, Raoult's law ...)
10) Solve set of linear equations (AX = B)
11) Solve non linear equations
12) Calculate volume roots of cubic equations of state
13) Set up and solve problems in enzyme kinetics (set of ordinary differential equations, Michaelis Menten form, etc)
14) Solve problems involving filtration (Darcy's Law)

And now for some "X"'s I have a very limited experience with/written software for

15) Read an image (tiff, jpg, png) - and run filters (low pass, high pass, band pass)
16) Locate spots on an image (microarray analysis of tiff images - locate center of spot, determine background intensities)
16) BLAST sequences at the NCBI - parse output according to defined criteria
17) Align two sequences using dynamic programming techniques (SmithWaterman (local) and Needleman Wunsch (global)

Beginner- Questions about a code

I am trying to make a program that asks questions and allows the user to answer them. When I try to use raw_input it gives me an error. Can anyone tell me what I am doing wrong?

name = raw_input("What is your name?")
color = raw_input("What is your favorite color?")

print = ("So your name is %s and your favorite color is %s." % (name, color))

I would like for it to allow the user to enter their name and favorite color and the output include the sentence with the information.

I have read online that raw_input might not work anymore but input did not allow me to answer to questions.

June 14, 2016 (What we did) (sort of did)

I was glad to see many pythonistas - welcome.

Reminder - come with/post problems, questions - "How do do X" or "Y" in python

My objective is not to "formally" teach python - but help you help yourself with python - and sure, I (and many others) can help you get to a point where you are comfortable with writing python scripts

(if you are reading this, post on what you heard/what you would like to hear/learn)

Tuesday June 14 2016 (Change of Venue)

Just a reminder

Tomorrow (June 14, 2016) we meet in the

auditorium at the

HudsonAlpha Institute for Biotechnology

http://hudsonalpha.org/directions

(Just come on in - sign in at the desk/as guest (if you do not see anyone, just
go to the auditorium)

WIndows packages for download

http://www.lfd.uci.edu/~gohlke/pythonlibs/  (windows packages)

Where to on June 14, 2016?

Please let us know/post where we should be spending our time on next Tuesday!